|
| Status |
Public on Feb 13, 2013 |
| Title |
ChIP-seq_ZFP143_Fibro |
| Sample type |
SRA |
| |
|
| Source name |
Mouse embryonic fibroblast cell line
|
| Organism |
Mus musculus |
| Characteristics |
cell line: MEF-like
chip antibody: ZNF143, rabbit polyclonal raised against a C-terminal epitope of ZNF143 (Myslinski et al JBC 2006)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP assays were performed essentially as previously described (Myslinski et al. 2006) with 1-4x107 cells. The chromatin was sonicated to an average of 200bp using a BioruptorTM UCD-200 (Diagenode) at Maximum power level for 30 minutes (pulses of 30 seconds with 30 seconds breaks). The immunoprecipitation step was performed with 5µg of specific antibodies. DNA purification steps were done using the MinElute PCR purification kit (Qiagen, cat. No. 28004) or using the classical phenol/chloroform extraction protocol. ChIP-seq library preparation was performed using illumina TruSeq DNA Sample Prep Kits according to manufacturer protocol.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Basecalls performed using Illumina CASAVA version 1.7 or v1.8
ChIP-seq reads were aligned to the hg19 or mm9 genome using Illumina software ELAND or Bowtie v0.12.7.
ChIP-seq peak calling was performed using MACS v1.4
Genome_build: hg19 and mm9
Supplementary_files_format_and_content: Wig files were generated using MACS v1.4 (10bps resolution).
|
| |
|
| Submission date |
Jul 11, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
PHILIPPE CARBON |
| Organization name |
IBMC
|
| Department |
UPR9002 ARN du CNRS
|
| Street address |
15 rue René Descartes
|
| City |
Strasbourg |
| ZIP/Postal code |
67084 |
| Country |
France |
| |
|
| Platform ID |
GPL11002 |
| Series (1) |
| GSE39263 |
Modulation of gene expression by ZNF143, THAP11 and NOTCH1 via overlapping binding sites in mammalian cells |
|
| Relations |
| SRA |
SRX159137 |
| BioSample |
SAMN01087348 |
